Urgent! Emails from internal user are put in Junk Folder

After upgrade, we observe some emails from a few internal users are put in Junk folder in recipient's email account. We tried to mark the sender is safe in Zimbra-Outlook, but we still see the emails are put in recipient's junk folder.

You need to look at the headers of the emails being sent to the Junk folder and see what the scoring is, you can also post the headers here and search the forums for some of the scoring settings.

Thank you phoenix. I have reset the score setting back to zcs6.0.6 level and commented "DOS_OUT_LOOK_TO_MX". Don't know if this will fix the issue completely?

I observed a interesting thing, this issue only happened on a few internal users in remote location. If I sent test emails from their zimbra-outlook or zimbra webmail here, the mails were not marked as Junk.

You didn't post details, but chances are you need to turn off the "X-Originating-IP headers" in the Zimbra Admin Console. This just got bad fairly recently (6.0.6 I think? maybe 6.0.7). There's a bug about it:

It's honestly fairly outrageous that something hasn't been done about this by now. It means that in Zimbra's default config (with X-Originating-IP turned on), it literally junks every single mail sent from your own users when they're logged in remotely via Outlook+ZCO. DOS_OUTLOOK_TO_MX + RCVD_IN_PBL (which will be the case assuming they're on a broadband ISP) alone produce enough score to junk a mail. It makes no sense that either rule would be counted against a message sent directly into the server from one of your own local users. I understand Zimbra doesn't write SpamAssassin or its rules, but that's really not a good enough excuse for a product like Zimbra.